Chronotype refers to individual preference in circadian cycles and is associated with psychiatric problems. Although previous research has demonstrated the influence of chronotype on cognitive function and brain structure in adults, little is known regarding the effects in children. Data from 4493 children (mean age of 143.06 months) from the Adolescent Brain Cognitive Development Study were obtained, wherein chronotype was assessed by the Munich Chronotype Questionnaire. Subsequently, the associations between chronotype, cognitive function, and regional brain volumes were evaluated using linear mixed-effects models. Behaviorally, chronotype was negatively associated with vocabulary knowledge and episodic memory performance. Based on these findings, the region of interest analysis revealed a negative association between chronotype, and left precentral gyrus, right superior parietal cortex, and posterior cingulate cortex volumes; moreover, precentral gyrus and posterior cingulate cortex were positively associated with vocabulary knowledge and episodic memory performance, respectively. These results indicate that, in children, the association between late chronotype, and volume reduction in the precentral gyrus and posterior cingulate cortex may be related to a reduction in vocabulary and episodic memory skills. This leads us to suggest that late chronotype may have a negative impact on brain health during childhood.